Question: Error downloading TCGA miRNA expression data
0
gravatar for JYBH0
19 months ago by
JYBH00
Imperial College London
JYBH00 wrote:

Hi,

I am trying to download miRNA expression data for Ovarian Cancer using TCGAbiolinks' GDCquery. I used the commands below few months ago for Prostate cancer dataset and it was working then. It doesn't work for prostate cancer now either. 

query <- GDCquery(project = "TCGA-OV",
                  data.category = "Transcriptome Profiling",
                  data.type = "miRNA Expression Quantification")

GDCdownload(query)
counts <- GDCprepare(query)

Error in grepl("miRNA", data.type, ignore.case) : 
  object 'ignore.case' not found

 

Can anyone help with solving this error? Thanks in advance !

tcgabiolinks • 359 views
ADD COMMENTlink modified 18 months ago by Levi Waldron980 • written 19 months ago by JYBH00

Hello,

 

There is no TARGET-OV in GDC. The code should be:

query <- GDCquery(project = "TCGA-OV",
                  data.category = "Transcriptome Profiling",
                  data.type = "miRNA Expression Quantification")

GDCdownload(query)
counts <- GDCprepare(query)
ADD REPLYlink written 19 months ago by tiagochst150

Hi yes, sorry, I did try 'TCGA-OV' and it still gives the same error. Previously, I was also trying to download 'TARGET- AML' hence copy and pasted the wrong code. I will edit my main post.

ADD REPLYlink written 19 months ago by JYBH00
Answer: Error downloading TCGA miRNA expression data
1
gravatar for Levi Waldron
18 months ago by
Levi Waldron980
CUNY Graduate School of Public Health and Health Policy, New York, NY
Levi Waldron980 wrote:

You might also try curatedTCGAData - it has an advantage of linking assays and clinical/pathological/specimen data in a MultiAssayExperiment. Here I obtain both the miRNA array and sequencing data in one MultiAssayExperiment:

> library(curatedTCGAData)
Loading required package: MultiAssayExperiment
> curatedTCGAData()
Please see the list below for available cohorts and assays
Available Cancer codes:
 ACC BLCA BRCA CESC CHOL COAD DLBC ESCA GBM HNSC KICH
 KIRC KIRP LAML LGG LIHC LUAD LUSC MESO OV PAAD PCPG
 PRAD READ SARC SKCM STAD TGCT THCA THYM UCEC UCS UVM 
Available Data Types:
 CNACGH CNASeq CNASNP CNVSNP GISTICA GISTICT
 Methylation miRNAArray miRNASeqGene mRNAArray
 Mutation RNASeq2GeneNorm RNASeqGene RPPAArray
> curatedTCGAData(diseaseCode = "OV")
                                 OV_CNACGH1                                  OV_CNACGH2 
       "OV_CNACGH_CGH_hg_244a-20160128.rda" "OV_CNACGH_CGH_hg_415k_g4124a-20160128.rda" 
                                  OV_CNASNP                                   OV_CNVSNP 
                   "OV_CNASNP-20160128.rda"                    "OV_CNVSNP-20160128.rda" 
                        OV_GISTIC_AllByGene                 OV_GISTIC_ThresholdedByGene 
         "OV_GISTIC_AllByGene-20160128.rda"  "OV_GISTIC_ThresholdedByGene-20160128.rda" 
                            OV_Methylation1                             OV_Methylation2 
     "OV_Methylation_methyl27-20160128.rda"     "OV_Methylation_methyl450-20160128.rda" 
                              OV_miRNAArray                             OV_miRNASeqGene 
               "OV_miRNAArray-20160128.rda"              "OV_miRNASeqGene-20160128.rda" 
                              OV_mRNAArray1                               OV_mRNAArray2 
           "OV_mRNAArray_huex-20160128.rda"       "OV_mRNAArray_TX_g4502a-20160128.rda" 
                              OV_mRNAArray3                                 OV_Mutation 
 "OV_mRNAArray_TX_ht_hg_u133a-20160128.rda"                  "OV_Mutation-20160128.rda" 
                         OV_RNASeq2GeneNorm                               OV_RNASeqGene 
          "OV_RNASeq2GeneNorm-20160128.rda"                "OV_RNASeqGene-20160128.rda" 
                               OV_RPPAArray 
                "OV_RPPAArray-20160128.rda" 
> curatedTCGAData(diseaseCode = "OV", assays = c("miRNAArray", "miRNASeqGene"), dry.run = FALSE)
snapshotDate(): 2018-05-08
snapshotDate(): 2018-05-08
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache 
    ‘/Users/lwaldron//.ExperimentHub/843’
harmonizing input:
  removing 8204 sampleMap rows not in names(experiments)
  removing 25 colData rownames not in sampleMap 'primary'
A MultiAssayExperiment object of 2 listed
 experiments with user-defined names and respective classes. 
 Containing an ExperimentList class object of length 2: 
 [1] OV_miRNAArray-20160128: SummarizedExperiment with 821 rows and 573 columns 
 [2] OV_miRNASeqGene-20160128: SummarizedExperiment with 705 rows and 461 columns 
Features: 
 experiments() - obtain the ExperimentList instance 
 colData() - the primary/phenotype DataFrame 
 sampleMap() - the sample availability DataFrame 
 `$`, `[`, `[[` - extract colData columns, subset, or experiment 
 *Format() - convert into a long or wide DataFrame 
 assays() - convert ExperimentList to a SimpleList of matrices
>
ADD COMMENTlink written 18 months ago by Levi Waldron980

Thanks for this solution. I tried it and I am able to download the miRseq data, but it seems like the data was curated in 2016 and has not been updated since? As I am able to download mRNA sequencing data from TCGAbiolinks, I wanted to compare their data and curatedTCCGAData's mRNA seq data, however I get another error while trying to download the data: 

data <- curatedTCGAData(diseaseCode = 'OV', assays =c('mRNAArray3'), dry.run = F)
Error in .searchFromInputs(assays, assaysAvail) :
  No matches found, modify search criteria

 

ADD REPLYlink modified 18 months ago • written 18 months ago by JYBH00
mRNAArray3 isn't one of the allowable assay types (mRNAArray is). curatedTCGAData provides the final Firehose pipeline snapshot. While GDC provides newer processing for some assays, there are no new data. >
ADD REPLYlink written 18 months ago by Levi Waldron980

Thanks that works! 

I also have a solution for my original question. I just updated the TCGAbiolinks package by downloading the development version straight from github:

devtools::install_github('BioinformaticsFMRP/TCGAbiolinks')
ADD REPLYlink written 18 months ago by JYBH00
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